Acute Encephalitis with Atypical Presentation
of Rubella in Family Cluster, India
Sumit D. Bharadwaj,1 Rima R. Sahay,1
Pragya D. Yadav, Sara Dhanawade,
Atanu Basu, Virendra K. Meena, Suji George,
Rekha Damle, Gajanan N. Sapkal
We report 3 atypical rubella cases in a family cluster in In-
dia. The index case-patient showed only mild febrile illness,
whereas the other 2 patients showed acute encephalitis and
died of the disease. We confirmed rubella in the index and
third cases using next-generation sequencing and IgM.
R ubella is usually considered a mild viral infection. Ap-
proximately 25%–50% of infections are asymptomatic
(1). Differential diagnosis of viral acute encephalitis syn-
drome (AES) caused by rubella, herpes simplex virus, mea-
sles, varicella zoster virus, and Epstein–Barr virus infec-
tions can be accomplished through the unique presentation
of rash in each case. Rubella typically presents as fever with
rash and is mostly diagnosed clinically, but rubella leading
to fatal AES is rare (1/6,000 cases) (2). A cluster of rubella-
associated encephalitis has been reported from Japan (3)
and rubella encephalitis without rash from Tunisia (4).
We report on rubella in 3 unvaccinated siblings in In-
dia. We investigated this family cluster at the request of
the treating physician in August 2017, on the eighth day
postinfection of the index case-patient.
The Study
The affected family belonged to a lower-middle-income
group in a village in Maharashtra, India. The father worked
as a ward attendant at a hospital, and the mother was a
homemaker. There were 3 children in the family; the index
rubella case-patient was a 7-year-old girl, who recovered
following a mild febrile illness. The 2 other siblings, an
8-year-old girl and a 2-year-old boy, died of acute encepha-
litis within 4 days of onset of disease (Figure). No history of
similar illness in the neighborhood, travel history, or visitors
were reported. There was also no history of consumption of
fruits or accidental ingestion of any toxic drugs or pesticides
Author affiliations: National Institute of Virology, Pune, India
(S.D. Bharadwaj, R.R. Sahay, P.D. Yadav, A. Basu, V.K. Meena,
S. George, R. Damle, G.N. Sapkal); Bharati Vidyapeeth
Deemed University Medical College and Hospital, Sangli,
India (S. Dhanawade)
DOI: DOI: https://doi.org/10.3201/eid2410.180053
Emerging Infectious Diseases • www.cdc.gov/eid • Vol. 24, No. 10, October 2018 1923
before symptom onset. Nutritional status for all children
was normal for height, weight, and body mass index.
The index case-patient developed a low-grade intermit-
tent fever; her temperature rose in the evening. The fever
subsided within 2 days after the patient took acetaminophen.
She had not been immunized against rubella. Her throat was
uncongested and there were no rashes or mucocutaneous le-
sions. Systematic examination revealed no abnormalities.
Biochemical tests were normal. Tests for dengue virus and
malarial parasites were negative. The child recovered with-
out any sequelae. The investigating team examined her on
the eighth day following onset of symptoms.
Two days following onset of illness in the index case-
patient, her 8-year-old sister developed a high-grade fever
and eye pain. There was no history of rash or mucocutane-
ous lesions. On day 2 of her illness, she had multiple epi-
sodes of convulsions with nonprojectile vomiting and was
admitted to a hospital. On day 3, she was put on a mechani-
cal ventilator, but she died that day. The cause of death was
cardiorespiratory failure with meningoencephalitis due to
intractable seizures. This child had not been immunized for
rubella; no clinical samples were available to test.
One day after the onset of fever in the second patient,
her 2-year-old brother developed a mild fever with no rash
or mucocutaneous lesions. His intermittent fever subsided
after he took acetaminophen. Two days later, he developed
a high-grade fever with convulsions and nonprojectile
vomiting. He became semiconscious, with decerebrated
rigidity. He became comatose and was put on mechanical
ventilation on day 4 of his illness. Plantar reflex was ab-
sent, and deep tendon reflexes were diminished. No car-
diovascular system abnormality was noted. His chest was
clear, with no wheeze or stridor. Abdominal examination
revealed no notable organomegaly. The child received an-
timicrobial drugs, phenytoin, mannitol, and acyclovir. He
died on day 5 of his illness. Details from the medical re-
cords for the second and third case-patients are provided in
online Technical Appendix 1 Table 1 (https://wwwnc.cdc.
gov/EID/article/24/10/18-0053-Techapp1.pdf).
We tested serum and urine samples from the index
case-patient and serum, urine, and cerebrospinal fluid (CSF)
samples from the third case-patient for Japanese encepha-
litis virus (5), West Nile virus (6), Chandipura virus (7),
and enteroviruses (8) using real-time quantitative reverse
1
These authors contributed equally to this article.
DISPATCHES

Figure. Timeline of clinical events

for 3 siblings infected with rubella
and encephalitis, India. *Negative
for Japanese encephalitis virus,
Chandipura virus, dengue virus,
West Nile virus, enterovirus,
and herpes simplex virus. CSF,
cerebrospinal fluid.

transcription PCR (qRT-PCR); for dengue, chikungunya, and
Zika viruses using CDC Trioplex qRT-PCR; and for rubella
using RT-PCR (9). We further used quantitative PCR to test
for varicella zoster virus DNA (10) and PCR for herpes sim-
plex virus 1 (Genekam Biotechnology, Duisburg, Germany,
No. K091). We also tested samples for rubella IgM and IgG
using a Siemens Healthcare Kit (Siemens, Erlangen, Ger-
many). We extracted RNA and DNA using a QIAAmp total
nucleic acid extraction kit (QIAGEN, Hilden, Germany).
We obtained a rubella nested PCR product of 185 bases
from a CSF sample from the third case-patient; no amplifi-
cation was obtained from serum and urine, so we used the
CSF sample for next-generation sequencing (11).We tested
serum samples from close contacts of the index and third
case-patients for the presence of rubella IgM and IgG (Table
1; online Technical Appendix 2, https://wwwnc.cdc.gov/
EID/article/24/10/18-0053-Techapp2.xlsx). We prepared
the RNA library following the defined protocol (12) using
a TruSeq Stranded mRNA Library preparation kit (Illumina,
San Diego, CA, USA); quantified it using a KAPA Library
Quantification Kit (Roche, Indianapolis, IN, USA); and
loaded it on an Illumina Miniseq NGS platform. We import-
ed raw RNA data of 147 MB in CLC Genomics Workbench
software (QIAGEN) for further analysis. We assembled the
RNA data using de novo and reference assembly methods
and obtained 1.9 million reads with an average length of 138
bp. From the total read, 0.57% mapped to the reference ge-
nome (GenBank accession no. JN635296) with an average
length of 123 bp. De novo assembly of reads gave 86 contigs
with an average length of 1,281 bp. Reference mapping led
to a ≈8 kb region (4.5 kb of nonstructural protein [NSP], 3
kb of structural protein [SP], and 0.5 kb in both NSP and SP
regions) that was broken intermittently (GenBank accession
nos. MG987207.1 for NSP and MG987208.1 for SP) (online
Technical Appendix 1 Figure 1). We used a 732-bp E1 gene
sequence to identify the rubella genotype (online Technical

Table 1. Laboratory investigations and results of the clinical samples of close contacts of case-patients with rubella and encephalitis in
a family cluster in India
Contact relationship to index Age, Contact with Anti-rubella IgM Anti-rubella
NIV no.* Specimen and third case-patients y/sex case-patients ELISA IgG ELISA
1730348 Serum Father 40/M All 3 Equivocal Positive
1730348-2 Serum Father 40/M All 3 Equivocal Positive
1730358 Serum Mother 27/F All 3 Negative Positive
1730358-2 Serum Mother 27/F All 3 Negative Positive
1730362 Serum Physician 38/F Index, 3rd Negative Positive
1730365 Serum Physician 32/F Index, 3rd Negative Positive
1730367 Serum Physician 25/F Index, 3rd Negative Positive
1730371 Serum Physician 26/F Index, 3rd Negative Positive
1730382 Serum Physician 26/F Index, 3rd Negative Positive
1730411 Serum Physician 25/F Index, 3rd Negative Positive
1730389 Serum Physician 26/F Index, 3rd Negative Positive
1730391 Serum Nursing staff 22/F Index, 3rd Positive Positive
1730394 Serum Nursing staff 25/F Index, 3rd Negative Positive
1730396 Serum Nursing staff 29/F Index, 3rd Negative Equivocal
1730398 Serum Paternal uncle 1 33/M Index, 3rd Negative Positive
1730374 Serum Paternal aunt 1 25/F Index, 3rd Negative Positive
1730933 Serum Paternal uncle 2 34/M Index, 3rd Negative Positive
1730936 Serum Cousin 11/M Index, 3rd Negative Positive
1730939 Serum Cousin 8/M Index, 3rd Negative Negative
1730941 Serum Paternal aunt 2 21/F Index, 3rd Negative Positive
1730944 Serum Grandfather 70/M Index, 3rd Negative Positive
1730948 Serum Grandmother 65/F Index, 3rd Negative Positive
1730950 Serum Paternal aunt 2 26/F Index, 3rd Negative Positive
*NIV, National Institue of Virology.

1924 Emerging Infectious Diseases • www.cdc.gov/eid • Vol. 24, No. 10, October 2018

Table 2. Rubella virus variability with respect to Indian strain
BAS*†
Intragroup variability, %
Genotype Nucleotide Amino acid
GI 6–9 1–2
GII 2–8 0–1
GIIA 8 0–1
GIIB 2–3 0–1
GIIC 7 0–2
NIV E1 gene 3 1
*GenBank accession no. AF039134.
†NIV, National Institue of Virology.
Appendix 1 Figure 1). The phylogenetic tree that we con-
structed revealed that this virus belongs to rubella genotype
2B (Table 2; online Technical Appendix 1 Figure 2).
Conclusions
Rubella encephalitis without identification of typical rubel-
la rash is rarely reported. In the cluster we describe, the par-
ents were asymptomatic and positive for anti-rubella IgG
when tested on the eighth day from the onset of symptoms
in the index case-patient. The rubella IgM equivocal status
of the father suggests that he could be a possible source of
infection to the family. His occupation as a hospital ward
attendant also indicates a possibility of infection either
through respiratory secretions or by contact with an infec-
tious agent on his body or on items carried to and from
his workplace. In rubella, neurologic symptoms most of-
ten occur 1–6 days after the onset of the exanthem (13). In
this cluster, rapid disease progression meant the second and
third case-patients died within 4 days of illness onset. The
index case-patient tested positive for rubella IgM on the
eighth day postinfection and the third case-patient tested
positive for rubella IgM on the fifth day postinfection, but
their specimens were negative for IgG, suggesting that the
children were not immunized and had not had any past ru-
bella infection. A serum sample from the index case-patient
from the 14th day postinfection was IgG positive. Through
epidemiologic linkage, the causative agent in the second
case may be similar to that for the other cases.
In conclusion, rubella encephalitis can present without
rash. Rubella virus infection should be considered in the
differential diagnosis of AES in unvaccinated children.
Acknowledgments
We gratefully acknowledge the guidance and technical expertise
provided by D.T. Mourya and B.V. Tandale throughout this
investigation. We also acknowledge support rendered by Pradeep
Awate and Milind Pore, by Bipin Telekar and Shiv Shankar
for assistance and outbreak logistics preparation, and by all the
staff of Virus Research and Diagnostic Laboratories, Japanese
Encephalitis, and BioSafety Level 4 laboratory for the technical
support. We acknowledge the Centers for Disease Control and
Prevention, Atlanta, GA, USA, for generously providing the
Trioplex reagents.
Emerging Infectious Diseases • www.cdc.gov/eid • Vol. 24, No. 10, October 2018 1925
Atypical Rubella in Family Cluster, India
About the Author
Dr. Bhardwaj and Dr. Sahay are medical scientists at the
National Institute of Virology, Pune, India, and are trained in
clinical and field epidemiology. Their research areas include
respiratory illness of viral origin and emerging and reemerging
viral infections as well as clinical and epidemiological
investigation of disease outbreaks.
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Address for correspondence: Gajanan N. Sapkal, National Institute of
Virology, Pune, 20-A, Dr. Ambedkar Road, Pune (Maharashtra), Pin
411001, India; email: gajanansapkalniv@gmail.com